Table 1. Average wall time required for common secondary structure prediction for 5S rRNA, tRNA, RNase P and SRP RNA homologous RNA sequence pairs.

	5S rRNA	tRNA	SRP RNA	RNase P RNA
Dynalign II	55 s	18 s	5 h:6 min:30 s	53 min:41 s
Dynalign	49 s	16 s	4 h:38 min:37 s	50 min:15 s

Four cores of a 12 core Intel Xeon E5–2695 v2 processor (2.4GHz) were used for parallel computations of RNase P RNA and SRP RNA sequence pairs. One core of an Intel Xeon E5–2695 v2 processor (2.4GHz) was used for computations of 5S rRNA and tRNA sequence pairs.